› 7qiz

Electron Microscopy
2.38Å resolution

Specific features and methylation sites of a plant 80S ribosome

Released:
DOI: 10.2210/pdb7qiz/pdb
PDB entry 7qiz coloured by chain, front view.
PDB entry 7qiz coloured by chain, side view.
PDB entry 7qiz coloured by chain, top view.
Source organism: Solanum lycopersicum
Primary publication:
Cryo-EM structure and rRNA modification sites of a plant ribosome.
Cottilli P, Itoh Y, Nobe Y, Petrov AS, Lisón P, Taoka M, Amunts A
OpenAccess logo Plant Commun 100342 (2022)
PMID: 35643637
Related structures: EMD-14004

Function and Biology Details

Reactions catalysed: 
Pectin + n H(2)O = n methanol + pectate
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 80-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-300333 (preferred)
Entry contents:
73 distinct polypeptide molecules
7 distinct RNA molecules
Macromolecules (80 distinct):
Large ribosomal subunit protein uL2 Chain: D
Molecule details ›
Chain: D
Length: 260 amino acids
Theoretical weight: 28.33 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: P29766 (Residues: 1-260; Coverage: 100%)
Gene names: RPL2, RPL8
Sequence domains:
Large ribosomal subunit protein uL4 C-terminal domain-containing protein Chain: F
Molecule details ›
Chain: F
Length: 406 amino acids
Theoretical weight: 44.85 KDa
Source organism: Solanum lycopersicum
UniProt:
  • Canonical: A0A3Q7HW81 (Residues: 1-406; Coverage: 100%)
Gene name: LOC101259570
Sequence domains:
Ribosomal protein L3 Chain: E
Large ribosomal subunit protein uL18 C-terminal eukaryotes domain-containing protein Chain: G
Large ribosomal subunit protein uL6 N-terminal domain-containing protein Chain: H
Thaliana 60S ribosomal protein L7 Chain: I
Ribosomal protein eL8/eL30/eS12/Gadd45 domain-containing protein Chain: J
Large ribosomal subunit protein uL6 alpha-beta domain-containing protein Chain: K
60S ribosomal protein L10 Chain: L
60S ribosomal protein L11 Chain: M
60S ribosomal protein L13 Chain: N
Large ribosomal subunit protein eL14 domain-containing protein Chain: O
Ribosomal protein L15 Chain: P
Pectinesterase Chain: Q
50S ribosomal protein L22, chloroplastic Chain: R
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: S
Ribosomal protein L19 Chain: T
60S ribosomal protein L18a Chain: U
60S ribosomal protein L21 Chain: V
60S ribosomal protein L22 Chain: W
60S ribosomal protein L23 Chain: X
TRASH domain-containing protein Chain: Y
60S ribosomal protein L23A Chain: Z
KOW domain-containing protein Chain: a
60S ribosomal protein L27 Chain: b
Large ribosomal subunit protein uL15/eL18 domain-containing protein Chain: c
60S ribosomal protein L29 Chain: d
60S ribosomal protein eL30 Chain: e
60S ribosomal protein L31 Chain: f
60S ribosomal protein L32 Chain: g
60S ribosomal protein L35a Chain: h
60S ribosomal protein L34 Chain: i
Similar to 60S ribosomal protein L35 Chain: j
60S ribosomal protein L36 Chain: k
Ribosomal protein L37 Chain: l
Large ribosomal subunit protein eL38 Chain: m
60S ribosomal protein L39 Chain: n
Ubiquitin-like domain-containing protein Chain: o
60S ribosomal protein L44 Chain: p
60S ribosomal protein L37a Chain: q
Ribosomal eL28/Mak16 domain-containing protein Chain: r
30S ribosomal protein S3, chloroplastic Chain: NA
Small ribosomal subunit protein uS7 domain-containing protein Chain: OA
Plectin/eS10 N-terminal domain-containing protein Chain: PA
40S ribosomal protein S15 Chain: QA
40S ribosomal protein S16 Chain: RA
40S ribosomal protein S18 Chain: TA
40S ribosomal protein S19 Chain: UA
Small ribosomal subunit protein uS10 domain-containing protein Chain: VA
40S ribosomal protein S28 Chain: WA
40S ribosomal protein S29 Chain: XA
mitogen-activated protein kinase Chain: YA
40S ribosomal protein S25 Chain: ZA
60S ribosomal protein L41 Chain: t
Small ribosomal subunit protein uS2 Chain: u
Small ribosomal subunit protein eS1 Chain: v
40S ribosomal protein S4 Chain: w
40S ribosomal protein S7 Chain: x
40S ribosomal protein S8 Chain: y
Small ribosomal subunit protein uS17 N-terminal domain-containing protein Chain: z
Small ribosomal subunit protein eS17 Chain: AA
40S ribosomal protein S21 Chain: BA
40S ribosomal protein S23 Chain: CA
40S ribosomal protein S26 Chain: DA
Small ribosomal subunit protein uS5 Chain: EA
40S ribosomal protein S6 Chain: FA
40S body ribosomal protein uS4 Chain: GA
Small ribosomal subunit protein uS15 N-terminal domain-containing protein Chain: HA
Ribosomal protein S14-like Chain: IA
40S ribosomal protein S24 Chain: KA
40S ribosomal protein S27 Chain: LA
40S ribosomal protein S30 Chain: MA
Small ribosomal subunit protein uS8c Chain: JA
tRNA Chain: s
25S ribosomal RNA Chain: 2
5S ribosomal RNA Chain: 5
5.8S ribosomal RNA Chain: 8
18S Chain: S2
tRNA_1 Chain: aA
Messenger RNA Chain: bA

Ligands and Environments

7 bound ligands:
Ligand K 119 x K
Ligand MG 364 x MG
Ligand ZN 6 x ZN
Ligand SPM 3 x SPM
Ligand SPD 1 x SPD
Ligand PUT 1 x PUT
Ligand BGC 1 x BGC
14 modified residues:
Ligand HIC 1 x HIC
Ligand THC 1 x THC
Ligand PSU 88 x PSU
Ligand OMU 28 x OMU
Ligand A2M 30 x A2M
Ligand OMG 25 x OMG
Ligand 1MA 1 x 1MA
Ligand OMC 21 x OMC
Ligand 5MC 2 x 5MC
Ligand UR3 1 x UR3
Ligand 7MG 1 x 7MG
Ligand 6MZ 1 x 6MZ
Ligand MA6 2 x MA6
Ligand IAS 1 x IAS

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 2.38Å
Relevant EMDB volumes: EMD-14004

Quick links

Citations

7 citation in other articles

Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.
Hassan et al. (2023)
6 more

1 mention without citation

Exploring N6-methyladenosine (m6A) modification in tree species: opportunities and challenges.
Ramakrishnan et al. (2024)